Gel electrophoresis is a ubiquitous technique in molecular biology research, pharmaceutical manufacturing, and other enterprises. The technique can be used to analyze the content of a biological sample or purify sufficient quantities of macromolecules from the sample for later use. Protein mixtures, peptide mixtures, and mixtures of DNA, RNA, and fragments of DNA and RNA can all be subjected to gel electrophoresis, which separates molecules from each other on the basis of molecular weight, charge, or other characteristics.
Slab-shaped gels are often used when multiple separations must be performed simultaneously, because these gels can accommodate multiple samples in parallel lanes. A slab-shaped gel is typically prepared by filling a mold with a gel precursor, which can be a solution containing a chemical such as acrylamide or agarose. A “comb” is then inserted in the mold, with teeth of the comb protruding into the gel precursor. After the gel is cast, such as by inducing polymerization of a chemical in the precursor, or allowing the precursor to cool and solidify, the comb is removed, resulting in indentations in one end of the gel that are the negative shapes of the comb teeth. These indentations serve as wells in which samples can be loaded, and the starting points for lanes in the gel that each accommodate one sample.
Electrophoresis is performed by positioning a loaded slab gel, still retained in the mold or now placed in another supporting structure, between two electrodes. The electrodes are energized to opposite polarities, and the flow of current between the electrodes causes molecules from the samples to enter and migrate through the gel at different rates. This process is colloquially called “running the gel.” The positions of the lanes along which the molecules migrate are determined by a number of factors, not all of which can be readily known or accounted for prior to running the gel. These factors include the positions of the wells into which the samples were loaded, the geometry of current flow (i.e., field lines) through the gel, and spatial variation in the composition of the gel. Uncertainty in the positions of lanes within a slab gel can be made worse by the impracticality of tracking molecules in real time as they migrate, and by the lack of physical segregation between lanes.
To harvest sample molecules from a slab gel, or characterize these molecules more extensively than is possible using electrophoresis alone, the techniques of electroelution or electroblotting are often performed after electrophoresis. These techniques require a current to be applied to the gel in a direction orthogonal to that used for electrophoresis, such that molecules arrayed in the gel migrate in a direction orthogonal to that achieved by electrophoresis and exit the gel. The molecules can then be collected on the surface of the gel (electroelution), or transferred to a membrane, where they can be reacted with binding partners and detected (electroblotting).
To prepare a slab gel for electroelution or electroblotting after electrophoresis, the gel typically must be removed from the structure in which electrophoresis was performed. This requires handling the gel, which is time consuming and can result in breakage, loss of portions of the samples, or loss of information about the positions of sample molecules within the gel. Because this information is anyway at best incomplete, due to uncertainty in where lanes of the gel are located, a membrane used for electroblotting must often cover a larger area of the gel than is occupied by molecules of interest. Detection of these molecules then requires larger amounts of binding partners and other reagents than would be necessary for a smaller membrane.